Today I felt much more comfortable and at ease. I no longer got lost when walking down the seemingly identical hallways to get to the Griffith Lab. I also ran into one of the other women who works in the same room as Dr. Bermek as I was walking in. She was really nice, and we had a short conversation as we were walking to the lab. It was a nice way to start the day. What I really like is all the other people working alongside Dr. Bermek are women. There is a great atmosphere in a place I thought would be strictly business. All the women I am surrounded by are extremely smart with many degrees. They all help each other out when they have questions about a protocol or need to borrow a pipette or gel lid. They also are always joking around with each other which I found really entertaining and funny. Once I walked in, Dr. Bermek and I, like every morning, made a plan for the day. I had a made a table of the amounts of supercoiled and relaxed DNA I counted on the EM on Tuesday. We took a look at the table and began calculating percentages of supercoiled vs relaxed DNA from the plain DNA sample, the UL8 sample, and the UL8 + CIP sample. I had a little bit of a hard time with the math at first but I caught on quickly. Once we finished calculating the percentages, we compared our results to the gel we had run the day before. The EM percentages were a good indicator of how the protein and CIP acted, but we also ran a gel because a lot of my counting and categorizing was personal based on which category I though the DNA would fall into. The results from the EM and the gel were pretty similar which was nice to see that I had counted somewhat correctly.
After we finished calculating the percentages of supercoiled vs. relaxed DNA, we checked on the agarose gel we had set up yesterday afternoon since it had finished being run and stained. The gel we ran was similar to another gel Dr. Bermek had already run, but she wanted more distinct bands, and on this gel, we tested time and concentration. Dr. Bermek thoroughly washed the gel with water because she knew she potentially wanted to use this gel for her paper, so she was very careful. Once Dr. Bermek saw the gel image she was jumping up and down with elation. She said it was one of the prettiest gels she had ever seen. The bands were really distinct which is exactly what she wanted. We were debating on whether to use a 0.6%, 0.8%, 0.9% or 1% gel, and we ended up settling on a 1% gel because of other protocols we had read online and it paid off. I, with a little bit of help from Dr. Bermek, made the gel that worked so well, so I was super excited. She told me “I need you here more often” which was a wonderful thing to hear. Dr. Bermek did not enjoy making agarose gels very much. When she showed the gel to one of the head guys in the lab, he also reiterated how nice the gel looked. Seeing the gel turn out so nicely made both Dr. Bermek’s and my day. We sat down and analyzed the gel. The basic conclusion we came too after a long conversation was the DNA began to relax with 75nM of the UL8 protein. With the reaction time gel we saw the protein began relaxing the DNA within only 15 seconds and the DNA became super relaxed in only two minutes.
After we finished analyzing the gel, we began to set up the next experiment. We were testing a drug used for the herpes simplex virus to see how it worked with the topoisomerase experiments we had been doing the past couple of days. Setting up the different amounts of each ingredient for the experiment required many calculations. I was nervous about all the math and didn’t fully catch onto everything. Each ingredient needed to be diluted which took at least 45 minutes to make all the dilutions. I helped Dr. Bermek with a couple of the dilutions, but she physically added all the ingredients into each tube. There were so many steps she let me sit down for a while and just watch her because of the complexity of the protocol. I am also much slower at pipetting than she is. Once she finished adding all the ingredients to the tubes, we had to wait awhile to incubate the samples. Dr. Bermek and I talked for a little while before it was time for me to go while we were waiting. It seemed like a little bit more of a relaxed day, but I still learned so much. It’s crazy how much knowledge I have obtained in just four days because I am immersed in each experiment. To me, working in a lab and learning about science is sort of like learning a foreign language. You have to immerse yourself and make mistakes in order to improve. I’m excited to rest up this weekend and recharge for another fun week!
The beautiful 1% gel I helped make being stained.
The wonderful results of the Agarose gel with very distinct bands.